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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
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<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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'meta_description' => 'Diagenode’s ATAC-seq kit provides a robust protocol for assessing genome-wide chromatin accessibility',
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'name' => 'Chromatin studies',
'description' => '<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p>Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective culture of merozoites paves the way to explore sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.</p>',
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
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<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
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<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
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<p class="p1">ATAC-seq, Assay for Transposase-Accessible Chromatin, followed by nextgeneration sequencing, is a key technology to easily identify the “open” regions of the chromatin, which are usually associated with permissive gene expression. Indeed, the nuclei of the samples are incubated with a transposase, and only the genomic regions associated with open chromatin will be accessible to this transposase. During the process those regions will be cut and sequencing adaptors will be added, allowing their sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only., giving a map of the chromatin status in the whole genome of the sample.</p>
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'description' => '<p><span>Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.</span></p>',
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'name' => 'In vitro production of cat-restricted Toxoplasma pre-sexual stages byepigenetic reprogramming',
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'description' => '<p>Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective culture of merozoites paves the way to explore sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.</p>',
'date' => '2023-01-01',
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Uncover transcription factor (TF) occupancy</li>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
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<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
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<ul type="”square”">
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<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p>Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective culture of merozoites paves the way to explore sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.</p>',
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
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<ul type="”square”">
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<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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<div class="row">
<div class="small-12 medium-8 large-8 columns"><br />
<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
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<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'authors' => 'Antunes A. V.et al.',
'description' => '<p>Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective culture of merozoites paves the way to explore sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.</p>',
'date' => '2023-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36711883',
'doi' => '10.1101/2023.01.16.524187',
'modified' => '2023-04-06 09:52:08',
'created' => '2023-02-21 09:59:46',
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View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
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<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
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<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<li> Uncover transcription factor (TF) occupancy</li>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
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<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
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<p><strong>ATAC-seq</strong>, Assay for<span> </span><strong>T</strong>ransposase-<strong>A</strong>ccessible<span> </span><strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the<span> </span><strong>transposase Tn5</strong><span> </span>which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
</div>
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<p>Diagenode’s<span> </span><b>ATAC-</b><b>seq</b><b><span> </span>kit<span> </span></b>is based on a highly validated protocol optimized for<span> </span><b>50,000<span> </span></b><b>cells</b><b><span> </span>per<span> </span></b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell<span> </span></b><b>requirement</b><b>:<span> </span></b><b>50,000<span> </span></b><b>cells /<span> </span></b><b>rxn</b></li>
<li><b>Robust protocol<span> </span></b>with<span> </span><b>high reproducibility<span> </span></b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong><span> </span>and<span> </span><b>efficient DNA capture<span> </span></b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids<span> </span></b><b>over-amplification</b></li>
<li>Allows adaptation/flexibility for<span> </span><b>more challenging samples<span> </span></b>to succeed with library prep.</li>
<li>Gives<span> </span><strong>early indication</strong><span> </span>if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p>Looking for ATAC-seq on tissue? Please, go to: <a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack:<span> </span><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"><span> </span>0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"><span> </span>(Tn5 transposase)<span> </span></a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"><span> </span>Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a><span> </span><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
</ul>',
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'meta_title' => 'ATAC-seq kit for open chromatin assessment C01080001 | Diagenode ',
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'meta_description' => 'Diagenode’s ATAC-seq kit provides a robust protocol for assessing genome-wide chromatin accessibility',
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<div class="small-12 medium-8 large-8 columns"><br />
<p>Chromatin structure plays a key role in regulating gene expression by allowing DNA accessibility to transcriptional machinery and transcription factors. The packaging of DNA into nucleosomes forms a closed structure that is not highly accessible to transcriptional elements whereas the open nucleosome structure allows DNA to be accessible. Diagenode offers a number of solutions to help you analyze chromatin and the role of transcriptional machinery including ChIP kits, ChIPmentation kits, antibodies, pA-Tn5 and ATAC-seq kits.</p>
</div>
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<p><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"><img src="https://www.diagenode.com/img/banners/b-microchip-category.png" /></a></p>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<div id="portal" class="main-portal">
<div class="portal-inner"><nav class="portal-nav">
<ul class="tips-menu">
<li><a href="#workflow" class="tips portal button" style="background: #13b29c; color: #f3fbfa;">Chromatin immunoprecipitation</a></li>
<li><a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation" class="tips portal button">ChIPmentation</a></li>
<li><a href="https://www.diagenode.com/en/categories/antibodies
" class="tips portal button">Antibodies</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">pA-Tn5</a></li>
<li><a href="https://www.diagenode.com/en/categories/atac-seq" class="tips portal button">ATAC-seq</a></li>
<li><a href="https://www.diagenode.com/en/categories/cutandtag" class="tips portal button">CUT&Tag</a></li>
</ul>
</nav></div>
</div>
<p>Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies that recognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci. ChIP can be used to compare enrichment of proteins, map protein modifications, or quantify a protein modification during a time course.</p>
<span class="anchor" id="workflow"></span>
<h4><span style="font-weight: 400;">The ChIP workflow</span></h4>
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><img src="https://www.diagenode.com/img/categories/kits_chromatin_function/website-chip-workflow.jpg" />
<div id="chip_workflow" class="content">
<div class="row">
<table>
<tbody>
<tr>
<td width="50%">
<h3 class="text-center">Step by step workflow</h3>
</td>
<td width="50%">
<h3 class="text-center">Optimal solution from Diagenode</h3>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>1.</strong><span> </span>Crosslink to bind proteins to DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-1-workflow.png" width="192" height="24" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/chip-cross-link-gold-600-ul">ChIP Cross-link Gold</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>2.</strong><span> </span>Shear DNA</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-2-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/p/bioruptor-pico-sonication-device#">Bioruptor<sup>®</sup><span> </span>Pico Sonication device</a></li>
<li><a href="https://www.diagenode.com/categories/chromatin-shearing">Shearing optimization reagent</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>3.</strong><span> </span>Immunoprecipitate with specific antibody</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-3-workflow.png" width="47" height="51" /></center></td>
<td>
<ul class="arrow">
<li><a href="https://www.diagenode.com/categories/chromatin-immunoprecipitation">ChIP-seq and ChIP-qPCR kits</a><span> </span>for transcription factors, histones, low inputs, plants</li>
<li><a href="https://www.diagenode.com/categories/chip-grade-antibodies">ChIP</a><span> </span>and<span> </span><a href="https://www.diagenode.com/categories/chip-seq-grade-antibodies">ChIP-seq grade</a><span> </span>antibodies</li>
<li><a href="https://www.diagenode.com/categories/ip-star">Automation available</a></li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>4.</strong><span> </span>Reverse crosslinks and purify</p>
<center><img src="https://www.diagenode.com/img/chip/step-by-step-4-workflow.png" width="194" height="80" /></center></td>
<td>
<ul class="arrow">
<li>Diagenode's ChIP kits (contain optimal purification modules)</li>
</ul>
</td>
</tr>
<tr>
<td colspan="2"></td>
</tr>
<tr valign="top">
<td>
<p class="lead text-center"><strong>5.</strong><span> </span><a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">ChIP-qPCR</a><span> </span>or ChIP-seq library preparation</p>
</td>
<td>
<ul class="arrow">
<li>ChIP-seq:</li>
</ul>
<ul style="list-style-type: square;">
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x48-12-indices-48-rxns">MicroPlex Library Preparation for 50 pg - 5 ng</a></li>
<li style="margin-left: 40px; font-size: 1.09rem;"><a href="https://www.diagenode.com/p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns">iDeal Library Preparation for > 5 ng</a></li>
</ul>
<ul class="arrow">
<li>ChIP qPCR</li>
</ul>
</td>
</tr>
</tbody>
</table>
</div>
</div>
</li>
</ul>
<p></p>
<h4><span style="font-weight: 400;">Products for chromatin study</span></h4>
<p><span style="font-weight: 400;"></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/crosslinking.png" alt="" width="35" height="35" /> Crosslinking<br /></b></span></strong><span style="font-weight: 400;">Efficient solution for protein-protein fixation.</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;"> <a href="../p/chip-cross-link-gold-600-ul
">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/chromatin-shearing.png" alt="" width="35" height="35" /> Chromatin shearing<br /></strong><strong><span style="font-weight: 400;">Perfectly sheared chromatin is critical for ChIP success.<span> </span><br /></span></strong><strong><a href="../categories/chromatin-shearing"><span style="font-weight: 400;">Read more</span></a><span style="font-weight: 400;"><span> </span>about solutions for successful chromatin preparation.<span> </span><br /></span></strong><strong><span style="font-weight: 400;"><a href="../categories/bioruptor-shearing-device">Read more</a><span> </span>about<span> </span></span><span style="font-weight: 400;">Bioruptor<span> </span></span><span style="font-weight: 400;">sonication.</span></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/immunoprecipitation.png" width="35" height="35" caption="false" /> Chromatin immunoprecipitation<br /></b></span></strong><span style="font-weight: 400;">Immunoprecipitation solutions for histone and transcription factor ChIP-qPCR and ChIP-seq for low inputs, plants, and animals including automated solutions</span><strong><span style="font-weight: 400;"><b><span style="font-weight: 400;">. <a href="../categories/chromatin-immunoprecipitation">Read more</a></span></b><br /></span></strong></p>
<p style="padding-left: 30px;"><strong><img src="https://www.diagenode.com/img/applications/ChIPmentation.png" alt="" width="35" height="35" /> ChIPmentation<br /><span style="font-weight: 400;">ChIPmentation, an exclusive technology, is an end-to-end ChIP-seq solution for low and difficult inputs. <a href="../categories/chromatin-ip-chipmentation">Read more</a></span><br /></strong></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-antibodies.png" alt="" width="35" height="35" /> ChIP and ChIP-seq antibodies<br /></b></span></strong><span style="font-weight: 400;">ChIP-grade antibodies are essential for success. <a href="../categories/antibodies">Learn more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-qPCR.png" width="35" height="35" caption="false" /> Primer pairs<br /></b></span></strong><span style="font-weight: 400;">Highly specific primer pairs for the amplification of the specific genomic regions. <a href="../categories/primer-pairs">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/cutandtag.png" width="35" height="35" caption="false" /> CUT&Tag solutions<br /></b></span></strong><span style="font-weight: 400;">An alternative to ChIP-seq that combines antibody-targeted controlled cleavage by a protein A-Tn5 fusion with NGS to identify the binding sites of DNA-associated proteins. <a href="../categories/cutandtag">Read more</a></span><span style="font-weight: 400;"><br /></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/dna-purification.png" width="35" height="35" caption="false" /> DNA purification<br /></b></span></strong><span style="font-weight: 400;"><a href="../categories/dna-and-rna-purification">Read more</a> about solutions for DNA purification</span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><span style="font-weight: 400;"><strong><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-seq.png" width="35" height="35" caption="false" /> Library preparation for ChIP-seq<br /></b></span></strong><span style="font-weight: 400;">Optimized solutions for the library preparation from low DNA input. <a href="../categories/library-preparation-for-ChIP-seq">Read more</a></span></span></span></p>
<p style="padding-left: 30px;"><span style="font-weight: 400;"><b><img src="https://www.diagenode.com/img/applications/ChIP-automation.png" alt="" width="35" height="35" /> ChIP and ChIP-seq automation<br /></b>Reproducibility, optimization simplicity, no variability. <a href="../categories/epigenetic-automation">Learn more</a></span></p>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<p class="text-justify">We offer <a href="https://www.diagenode.com/en/categories/chromatin-immunoprecipitation" target="_blank">complete ChIP kits</a> or <strong>individual kit components</strong> from antibodies, buffers, beads, chromatin shearing, and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="center" style="text-align: center;"><a href="../pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
</div>
</div>
</div>
<h4>Chromatin resources</h4>
<h3>Posters</h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibody-chipseq-qc-using-the-ipstar-compact-poster"><span style="font-weight: 400;">Understanding our antibody QC</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/antibodies-you-can-trust-poster"><span style="font-weight: 400;">High quality ChIP antibodies</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-kit-results-with-true-microchip-kit-poster"><span style="font-weight: 400;">ChIP with only 10,000 cells</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/high-resolution-chipseq-profiles-with-ipstar-automated-platform-poster"><span style="font-weight: 400;">High resolution ChIP-seq using automation</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/bioinformatics-pipeline-for-chipseq-analyses"><span style="font-weight: 400;">ChIP-seq bioinformatics</span></a></li>
</ul>
<h3><span style="font-weight: 400;">Application notes</span></h3>
<ul>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipettor-application-note"><span style="font-weight: 400;">Simple semi-automaton for easy and inexpensive ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chipseq-from-human-tumor-tissue"><span style="font-weight: 400;">Performing ChIP-seq on human tumor tissue</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/plant-chip-seq-application-note"><span style="font-weight: 400;">Plant ChIP-seq – a successful method</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/documents/chip-seq-application-note"><span style="font-weight: 400;">Best workflow practices for low input ChIP</span></a></li>
<li style="font-weight: 400;"><a href="https://www.diagenode.com/files/application_notes/AN-ChIP-Cas9-02_2018.pdf"><span style="font-weight: 400;">Optimize the selection of guide RNA by ChIP to keep CRISPR on-target</span></a></li>
</ul>
<h3>Publications related to ChIP</h3>
<ul>
<li><a href="https://www.diagenode.com/en/publications/view/3373">Corticosteroid receptors adopt distinct cyclical transcriptional signatures</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3347">Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes</a></li>
<li><a href="https://www.diagenode.com/en/publications/view/3355">Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile</a></li>
</ul>
<h3><span style="font-weight: 400;">Brochures</span></h3>
<ul>
<li><a href="https://www.diagenode.com/files/brochures/Chromatin_Immunoprecipitation_Brochure.pdf"><b>Chromatin </b><span style="font-weight: 400;">products brochure</span></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Epigenetic_Antibodies_Brochure.pdf"><span style="font-weight: 400;">Epigenetic<span> </span></span><b>Antibodies</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/Bioruptor_Sonicator_Brochure.pdf"><span style="font-weight: 400;">Bioruptor for<span> </span></span><b>chromatin shearing</b></a></li>
<li><a href="https://www.diagenode.com/files/brochures/IPStar_Automated_System_Brochure.pdf"><span style="font-weight: 400;">Automating<span> </span></span><b>ChIP</b><span style="font-weight: 400;"><span> </span>and<span> </span></span><b>ChIP-seq</b></a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
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<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
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<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
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<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
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<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
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<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
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<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
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'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
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<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/atacseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><strong>ATAC-seq</strong>, Assay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology for genome-wide mapping of accessible chromatin. The technology is based on the use of the <strong>transposase Tn5</strong> which cuts exposed open chromatin and simultaneously ligates adapters for subsequent amplification and sequencing. ATAC-seq methods allow you to:</p>
<ul>
<li> Gain insight into gene regulation and understand open chromatin signatures</li>
<li> Determine nucleosome positions at single nucleotide resolution</li>
<li> Uncover transcription factor (TF) occupancy</li>
</ul>
<p>The Diagenode’s <b>ATAC-</b><b>seq</b><b> kit </b>is based on a highly validated protocol optimized for <b>50,000 </b><b>cells</b><b> per </b><b>reaction</b>. The kit includes the reagents for cell lysis and nuclei extraction, tagmentation and DNA purification as well as for library amplification. The primer indexes for multiplexing are not included in the kit and must be purchased separately.</p>
<h4><span style="font-weight: 400;">ATAC-seq kit features:</span></h4>
<ul>
<li><b>Cell </b><b>requirement</b><b>: </b><b>50,000 </b><b>cells / </b><b>rxn</b></li>
<li><b>Robust protocol </b>with <b>high reproducibility </b>between replicates and repetitive experiments</li>
<li><strong>Easy</strong> and <b>efficient DNA capture </b>after the tagmentation reaction using Diagenode`s MicroChIP DiaPure columns (included)</li>
<li>Additional qPCR step to determine the number of cycles needed for library amplification: </li>
<ul type="”square”">
<li><b>Avoids </b><b>over-amplification </b></li>
<li>Allows adaptation/flexibility for <b>more challenging samples </b>to succeed with library prep.</li>
<li>Gives <strong>early indication</strong> if the experiment does not work (no qPCR amplification)</li>
</ul>
</ul>
<p><span>Looking for ATAC-seq on tissue? Please, go to: </span><a href="https://www.diagenode.com/en/p/ATAC-seq-package-tissue-C01080006">ATAC-seq package for tissue</a></p>',
'label1' => 'Method overview',
'info1' => '<p><strong>ATAC-seq</strong>, <strong>A</strong>ssay for <strong>T</strong>ransposase-<strong>A</strong>ccessible <strong>C</strong>hromatin, followed by next generation sequencing, is a key technology to easily identify the <strong>open regions of the chromatin.</strong> The protocol consists of <strong>3 steps</strong>: <strong>nuclei preparation</strong>, <strong>tagmentation</strong> and <strong>library amplification</strong>. First, the cells undergo the lysis, ending with the crude nuclei. Then, the nuclei are incubated with a tagmentase (Tn5 transposase), which cuts the genomic regions associated with open chromatin and inserts the sequencing adaptors. Finally, the generated libraries are amplified and can be used for sequencing. High-throughput sequencing will then detect peaks, in open regions of the chromatin only, giving a map of the chromatin status in the whole genome of the sample.</p>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-atac-seq.png" alt="ATAC-seq kit workflow" width="600px" caption="false" /></p>',
'label2' => 'Example of results',
'info2' => '<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig1.png" alt="library prepared with the Diagenode ATAC-seq kit " width="500px" caption="false" /></p>
<p><strong>Figure 1.</strong>Representative Bioanalyzer profile of an ATAC-seq library prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig2.png" alt="Diagenode ATAC-seq kit " caption="false" width="951" height="148" /></p>
<p><strong>Figure 2.</strong> Main ATAC-seq alignment and peak calling statistics of 3 replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells. (Mapping efficiency: Percentage of non-mitochondrial reads that mapped to the reference genome. Uniquely mapped ratio: Proportion of mapped reads that map to only one location on the reference genome (hg19). Peaks: Number of peaks (open chromatin regions) identified by MACS2 for each sample. FRiP - Fraction of reads in peaks: Percentage of reads in peaks, with respect to the number of uniquely mapped reads. Sequencing was realized in paired-end mode 50 base pairs (PE50) on an Illumina NovaSeq6000.)</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3a.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig3b.png" alt="Assay for Transposase-Accessible Chromatin" width="500px" caption="false" /></p>
<p><strong>Figure 3</strong> Sequencing profiles of ATAC-seq library (3 replicates) prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>
<p><img src="https://www.diagenode.com/img/product/kits/atacseq-fig4.png" alt=" open chromatin regions" caption="false" width="383" height="739" /></p>
<p><strong>Figure 4. </strong><br /> Heatmap around TSS of three ATAC-seq replicates prepared with the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No. C01011034) on 50,000 nuclei from K562 cells.</p>',
'label3' => 'Additional solutions for ATAC-seq kit',
'info3' => '<p><a href="https://www.diagenode.com/en/categories/primer-indexes-for-tagmented-libraries">Primer indexes for tagmented libraries</a></p>
<p>Magnetic rack: <a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit">DiaMag</a><a href="https://www.diagenode.com/en/p/diamag02-magnetic-rack-1-unit"> 0.2 ml – Cat. No. B04000001</a></p>
<p>Additional supplies (included in the kit and available separately):</p>
<ul>
<li><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">Tagmentase</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30"> (Tn5 transposase) </a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">loaded</a><a href="https://www.diagenode.com/en/p/tagmentase-loaded-30">, Cat. No. C01070012</a></li>
<li><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x">Tagmentation</a><a href="https://www.diagenode.com/en/p/tagmentation-buffer-2x"> Buffer (2x), Cat. No. C01019043</a></li>
<li><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">MicroChIP</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">DiaPure</a> <a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">columns</a><a href="https://www.diagenode.com/en/p/microchip-diapure-columns-50-rxns">, Cat. No. C03040001</a></li>
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'description' => '<p>Sexual reproduction of , which is restricted to the small intestine of felids, is sparsely documented, due to ethical concerns surrounding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described . In this study, we found that transcription factors AP2XII-1 and AP2XI-2, expressed in tachyzoite stage that causes acute toxoplasmosis, can silence genes necessary for merozoites, a developmental stage critical for sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a drastic change in the transcriptional program, promoting a complete transition from tachyzoites to merozoites. Pre-gametes produced under these conditions are characterized by specific protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit the epigenitors MORC and HDAC3 , which in turn restrict the accessibility of chromatin to the transcriptional machinery. Thus, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. This effective culture of merozoites paves the way to explore sexual reproduction without the need to infect kittens and has potential for the development of therapeutics to block parasite transmission.</p>',
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